Mermaid Whole Genome Assembler
C++ C
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Latest commit da56dae Nov 12, 2012 Richard Xia Merge pull request #3 from maxfeldman14/master
renamed and populated conf example
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Makefile
README.md
TODO
bam_reader.cpp
bam_reader.h
base.cpp
base.h Separated KmerCountStore to 2 parts May 4, 2012
bloom_filter.cpp
bloom_filter.h
config.cpp
config.h
contig.cpp
contig.h Do not modify contigs KmerContigMap May 8, 2012
contig_store.cpp
contig_store.h
exceptions.h Copied cpp code from other repo Apr 5, 2012
fastq_reader.cpp
fastq_reader.h
hash_map.h
kmer.cpp
kmer.h
kmer_contig_map.cpp
kmer_contig_map.h
kmer_count_map.cpp Updated configuration usage. Nov 8, 2012
kmer_count_map.h
kmer_ext_map.cpp
kmer_ext_map.h
lookup3.cpp
lsh.cpp
lsh.h Added LSH based on shingles Apr 24, 2012
main.cpp
mermaid.conf.example
nethub.cpp Fixed nethub multi-buffer bug May 4, 2012
nethub.h Started implementing gather_contigs May 1, 2012
reader.cpp
reader.h Copied cpp code from other repo Apr 5, 2012
scalable_bloom_filter.cpp
scalable_bloom_filter.h
utils.cpp Copied cpp code from other repo Apr 5, 2012
utils.h

README.md

Prerequisites

MERmaid only has three main dependencies:

  • Boost C++: Base, MPI and filesystem
  • An MPI framework: We only test it with openmpi
  • Google sparsehash

Currently, we are only running it on 64-bit Linux. Mac OS X is known to have problems building.

Building

Just run make in the top-level directory.

Running

./mermaid output-file-prefix input-files ..

input-files must be a list of FASTQ files using the Illumina 1.3 quality score format

The outputs will be

  • A set of files containing lists of initial k-mers after the initial counting phase. These will be named output-file-prefix.ufx.
  • A file containing all the contigs. This will be named output-file-prefix.contigs.0

Mermaid will override default configurations if they are specified in "mermaid.conf". Copy mermaid.conf.example to mermaid.conf and adjust parameter values to override defaults.

TODO

Verify that this README is correct